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- PDB-9g4q: Crystal structure of the salivarius-1 RNA motif -

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Basic information

Entry
Database: PDB / ID: 9g4q
TitleCrystal structure of the salivarius-1 RNA motif
ComponentsRNA (52-MER)
KeywordsRNA / RNA structure / tRNA-mimicking / X-ray crystallography
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesLigilactobacillus salivarius UCC118 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: To Be Published
Title: Structural basis for tRNA-mimicking by salivarius-1 RNA motif
Authors: Huang, L. / Lilley, D.M.J.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (52-MER)
B: RNA (52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8518
Polymers33,6462
Non-polymers2056
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-17 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.409, 68.094, 99.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (52-MER)


Mass: 16822.797 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Ligilactobacillus salivarius UCC118 (bacteria)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.04 M Magnesium Acetate, 0.05 M Sodium Cacodylate pH 6.0, 30% v/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9198 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.99→56.17 Å / Num. obs: 44110 / % possible obs: 100 % / Observed criterion σ(I): 1.4 / Redundancy: 25.3 % / CC1/2: 1 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.022 / Net I/σ(I): 15.6
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 25.8 % / Rmerge(I) obs: 3.504 / Num. unique obs: 1125 / CC1/2: 0.68 / Rpim(I) all: 0.697 / % possible all: 98.51

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Processing

Software
NameVersionClassification
xia2data reduction
xia2data scaling
PHENIXphasing
PHENIX(1.14_3260: ???)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.99→44.24 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.26
RfactorNum. reflection% reflection
Rfree0.255 2245 5.09 %
Rwork0.225 --
obs0.226 44110 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2207 6 44 2257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022465
X-RAY DIFFRACTIONf_angle_d1.023841
X-RAY DIFFRACTIONf_dihedral_angle_d14.7531239
X-RAY DIFFRACTIONf_chiral_restr0.127516
X-RAY DIFFRACTIONf_plane_restr0.002103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.0330.41181200.41482596X-RAY DIFFRACTION98
2.033-2.08020.3791560.39552607X-RAY DIFFRACTION100
2.0802-2.13230.44061400.35992644X-RAY DIFFRACTION100
2.1323-2.18990.34021170.3372634X-RAY DIFFRACTION100
2.1899-2.25440.36081440.33222637X-RAY DIFFRACTION99
2.2544-2.32710.41441210.33372637X-RAY DIFFRACTION100
2.3271-2.41030.42751590.3192632X-RAY DIFFRACTION100
2.4103-2.50680.36031280.34442632X-RAY DIFFRACTION100
2.5068-2.62080.29421330.30412637X-RAY DIFFRACTION100
2.6208-2.7590.38021270.31232628X-RAY DIFFRACTION100
2.759-2.93180.30971340.29652641X-RAY DIFFRACTION100
2.9318-3.15810.28921260.24262643X-RAY DIFFRACTION99
3.1581-3.47580.25351790.2012566X-RAY DIFFRACTION99
3.4758-3.97850.21231520.17552622X-RAY DIFFRACTION100
3.9785-5.01140.18011700.15032624X-RAY DIFFRACTION100
5.0114-44.240.19791390.16312485X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4215-0.4841-0.43120.79231.62573.5756-0.25170.0409-0.41540.2263-0.2206-0.03171.5245-0.29030.44850.639-0.02810.05220.4534-0.05310.478519.196321.95946.028
22.3470.8547-1.91271.4051-0.04712.981-0.0177-0.28330.0264-0.1165-0.00420.12050.63860.06070.09370.4988-0.09590.00620.4521-0.01890.372317.487329.027257.8132
32.76460.36690.71663.03280.72715.28930.0415-0.16910.1052-0.2281-1.5775-1.99831.32961.5781.52081.36320.44060.16751.26180.32221.003928.429614.848857.6949
41.84330.4242-1.36870.21780.01022.65520.0081-0.072-0.16830.06530.1262-0.15610.4180.6255-0.03990.42340.0384-0.02040.4639-0.01380.381125.271631.049839.8728
53.0032-0.4764-0.16871.01810.84071.31570.7434-0.60810.07290.1462-0.452-0.0426-0.1754-0.2480.1810.4505-0.0449-0.01720.6764-0.01450.517819.173430.1326.7926
61.2690.1653-0.45810.1239-0.44881.2385-0.1647-0.30420.33580.14570.03350.1412-0.59090.16890.16510.46590.0001-0.06640.61980.07970.508229.796531.462-13.0058
71.8905-0.47281.01540.0898-0.25020.5301-0.18731.0765-0.1551-0.107-0.096-0.35960.13830.44580.30660.4954-0.00370.00260.88330.03860.476428.322535.0623-28.6142
82.24340.31791.30832.9276-2.41394.33720.02930.7204-0.1742-0.401-0.2229-0.1790.1140.70460.08370.362-0.010.00050.5081-0.04980.374718.001430.9355-22.5232
92.4145-1.1313-1.53112.4662-0.11881.3269-0.15480.917-1.2745-0.404-0.4860.63840.6973-0.3720.64920.61550.19050.02180.94230.02980.809835.177225.2094-22.3813
102.37990.7178-1.95781.0409-1.20661.9954-0.4025-0.4377-0.50970.28490.0325-0.3140.31020.50860.26540.52430.035-0.03760.55520.10450.581528.709521.3976-5.1398
112.426-0.4872-1.10940.763-0.73891.7663-0.0799-0.0318-0.5331-0.049-0.00390.0990.4072-0.2859-0.00720.4334-0.0332-0.0030.4728-0.04920.485613.782921.6123-14.1885
122.8967-0.3477-1.18870.7083-0.5472.03130.2163-0.972-0.23860.19520.0911-0.31070.18060.2444-0.07590.40420.0263-0.04310.59250.04640.448518.590425.8994.727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 1 THROUGH 16 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 17 THROUGH 21 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 22 THROUGH 26 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 27 THROUGH 52 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 1 THROUGH 6 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 7 THROUGH 11 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 12 THROUGH 16 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 17 THROUGH 21 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 22 THROUGH 26 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 27 THROUGH 31 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 32 THROUGH 41 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 42 THROUGH 52 )

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